Network Projects
| Name | Method | Description |
|---|---|---|
| Arabidopsis thaliana GIL-Hive Co-expression Network v1 | RMTGeneNet |
A Gene Interaction Layer (GIL) Hive is a collection of networks constructed after clustering of input samples. Each cluster is then used to create a unique network. For this project a GIL-Hive was constructed for Arabidopsis thaliana using all available Affymetrix samples from the GPL198 platform at the time. This resulted in 90 distinct networks. |
| Arabidopsis thaliana Global Co-expression Network v1 | RMTGeneNet |
A gene co-expression network for Arabidopsis thaliana. The network was constructed using all public Affymetrix microarrays from the NCBI GEO platform GPL198 at the time. |
| Arabidopsis thaliana Tissue Co-expression Network Compendium v1 | RMTGeneNet |
For this project all available Affymetrix micorarrays for Arabidopsis thaliana from the platform NCBI GEO GPL198, were manually organized into tissue specific groups. Each group underwent network construction. |
| Functional Enrichment of A. thaliana Global, Tissue and K90 GIL networks | In-house perl script |
The Feltus-lab in-house enrichment Perl script (modeled after DAVID) was used for testing functional enrichment of InterPro... |
| Functional Enrichment of A. thaliana Global v1.0 network | In-house perl scrip |
The Feltus-lab in-house enrichment Perl script (modeled after DAVID) was used for testing functional enrichment of InterPro. |
| Functional Enrichment of A. thaliana K90 GIL networks | In-house perl script |
The Feltus-lab in-house enrichment Perl script (modeled after DAVID) was used for testing functional enrichment of InterPro... |
| Import of dbSNPs for Arabdidopsis, Zea Mays and Oryza sativa | manual download & processing |
SNPs were downloaded in bulk from the NCBI dbSNP FTP repository for Arabidopsis thaliana, Oryza sativa and Zea Mays in XML format. The XML was coverted to FASTA formatted files containing the SNP and 5' and 3' flanking sequences. These sequences were aligned to the TAIR10, Rice MSU v6.0, and the MaizeSequence.org B73 genome assemblies respectively using blat. Only SNPs that mapped uniquely along the full length of the flanking sequence were kept and uploaded to this database. |
| Maize B73 Genes | Manual download from maizesequence.org |
Gene predictios from the filtered set of the B73 Zea mays genome. Sequences were downloaded from the maizesequence.org FTP site. |
| MSU v6.0 Oryza sativa whole genome download | Manual Download | |
| MSU v7.0 Oryza sativa whole genome download | Manual Download |